Contacts of the helix formed by residues 96 - 111 (chain C) in PDB entry 2GTP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 96 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C GLY* 4.5 2.7 - - - +
90C LEU* 3.7 13.2 + - + -
91C LYS* 3.9 47.7 - - + +
94C PHE* 3.5 14.6 - - - -
95C SER* 1.3 83.0 + - - +
97C GLU* 1.3 68.9 + - - +
98C ASN 3.1 2.9 + - - -
99C ILE* 3.3 11.0 - - + +
100C GLU* 3.0 42.7 + - + +
134C LYS* 4.9 11.1 - - - +
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Residues in contact with GLU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR* 3.7 8.7 + - - -
206B SER* 5.0 0.2 + - - -
207B GLU* 4.5 2.9 - - - +
210B LYS* 2.6 42.5 + - - -
94C PHE 3.9 0.5 - - - +
95C SER* 3.4 9.8 - - - -
96C GLU* 1.3 84.2 + - - +
98C ASN* 1.3 69.9 + - - +
100C GLU* 3.7 11.5 - - - +
101C PHE* 2.9 31.0 + - - +
127C PHE* 4.1 2.1 - - - -
134C LYS* 3.8 42.8 - - + +
135C GLN 4.0 15.3 - - - +
136C ILE* 4.1 5.5 - - + +
137C ASN 5.0 1.7 + - - -
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Residues in contact with ASN 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B THR* 3.5 31.7 + - - +
90C LEU* 4.9 0.9 - - + +
95C SER* 3.2 12.3 + - - +
96C GLU 3.1 1.0 - - - -
97C GLU* 1.3 87.2 + - - +
99C ILE* 1.3 57.6 + - - +
101C PHE* 3.4 3.1 + - - +
102C TRP* 2.9 24.6 + - - +
136C ILE* 4.1 6.8 - - - +
137C ASN* 4.5 1.6 + - - +
165C ILE* 3.4 48.4 - - + +
168C LEU* 3.5 19.5 - - - +
169C MET* 3.8 18.8 - - + +
173C SER* 5.1 0.4 + - - -
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Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LEU* 3.8 19.7 - - + -
83C GLN* 3.5 30.3 - - + +
86C PHE* 3.8 22.9 - - + -
87C GLY* 4.1 12.8 - - - +
90C LEU* 3.6 18.7 - - + +
96C GLU* 3.3 16.0 + - + +
98C ASN* 1.3 74.5 - - - +
100C GLU* 1.3 70.7 + - + +
102C TRP* 3.5 6.8 - - + +
103C LEU* 2.9 50.8 + - + +
169C MET* 3.9 10.6 - - - -
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LYS* 5.7 3.6 + - - -
96C GLU* 3.0 46.5 + - + +
97C GLU* 3.6 8.3 + - - +
99C ILE* 1.3 83.5 - - + +
101C PHE* 1.3 58.4 + - - +
103C LEU* 3.4 10.4 + - + +
104C ALA* 2.9 28.4 + - - +
127C PHE* 3.9 16.6 - - + -
134C LYS* 3.7 26.3 + - - +
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Residues in contact with PHE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C GLU 2.9 19.0 + - - +
98C ASN 3.5 3.6 - - - +
100C GLU* 1.3 74.1 - - - +
102C TRP* 1.3 70.2 + - - +
104C ALA* 3.1 3.6 + - - +
105C CYS* 2.9 49.1 + - - -
123C ILE* 3.9 17.7 - - + -
127C PHE* 3.6 30.0 - + + -
128C VAL* 4.1 14.4 - - + -
136C ILE* 3.6 29.6 - - + -
158C PHE* 4.5 5.2 - + - -
161C ALA* 3.8 33.4 - - + -
162C GLN* 3.8 2.2 - - - -
165C ILE* 3.8 20.6 - - + -
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Residues in contact with TRP 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 3.9 45.1 - - + -
83C GLN* 4.1 11.9 - - - -
98C ASN 2.9 13.8 + - - +
99C ILE* 3.5 11.7 - - + +
101C PHE* 1.3 79.7 - - - +
103C LEU* 1.3 84.0 + - + +
105C CYS 3.2 2.1 + - - -
106C GLU* 3.1 48.9 + - + +
162C GLN* 3.2 47.9 + - + +
165C ILE* 5.3 1.6 - - + -
166C TYR* 3.7 26.1 - + + +
169C MET* 4.2 18.4 - - + -
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C GLN* 3.7 35.0 - - + +
99C ILE* 2.9 38.5 + - + +
100C GLU* 3.8 9.0 - - + +
102C TRP* 1.3 95.0 - - + +
104C ALA* 1.3 65.0 + - - +
106C GLU* 3.3 8.1 + - + +
107C ASP* 3.1 24.6 + - - +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLU 2.9 14.7 + - - +
101C PHE 3.1 8.5 + - - +
103C LEU* 1.3 77.6 - - - +
105C CYS* 1.3 55.7 + - - +
107C ASP* 3.5 7.4 + - - +
108C TYR* 2.9 28.9 + - - +
123C ILE* 3.5 21.7 - - + +
127C PHE* 3.7 24.9 - - + -
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Residues in contact with CYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PHE* 2.9 56.0 + - - -
102C TRP 3.5 7.4 - - - +
104C ALA* 1.3 72.9 - - - +
106C GLU* 1.3 65.4 - - - +
108C TYR* 3.1 8.6 + - - +
109C LYS* 2.9 31.1 + - - +
123C ILE* 4.9 1.6 - - - -
158C PHE* 3.6 24.2 - - + -
162C GLN* 3.6 26.2 - - + +
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TRP* 3.1 51.5 + - + +
103C LEU* 3.3 11.9 + - + +
105C CYS* 1.3 76.5 - - - +
107C ASP* 1.3 62.2 + - - +
109C LYS* 3.1 35.1 + - - +
110C LYS* 3.3 17.1 + - - +
162C GLN* 3.0 19.7 + - - +
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Residues in contact with ASP 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU 3.1 14.0 + - - +
104C ALA* 3.8 7.1 - - - +
106C GLU* 1.3 78.2 - - - +
108C TYR* 1.3 63.3 + - - +
110C LYS* 3.1 9.8 + - - +
111C THR* 2.8 29.1 + - - -
119C LYS* 3.8 22.9 - - - +
123C ILE* 5.7 0.9 - - - +
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Residues in contact with TYR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ALA 2.9 20.0 + - - +
105C CYS* 3.1 7.6 + - - +
107C ASP* 1.3 79.4 - - - +
109C LYS* 1.3 62.4 - - + +
111C THR* 3.2 20.5 + - - -
116C LEU* 3.6 32.2 - - + +
119C LYS* 3.6 20.6 - - + -
120C ALA* 3.5 23.8 - - + -
123C ILE* 3.7 8.5 - - + -
153C PRO* 3.3 23.4 - - - +
154C THR 3.0 28.3 + - - -
155C PRO* 3.7 19.6 - - + +
157C CYS* 3.6 4.9 - - + +
158C PHE* 3.7 30.7 - + + -
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C CYS* 2.9 19.4 + - - +
106C GLU* 3.1 31.9 + - - +
107C ASP 3.2 0.4 - - - -
108C TYR* 1.3 78.4 - - + +
110C LYS* 1.3 61.6 + - + +
111C THR 3.5 5.5 + - - +
155C PRO* 3.6 37.2 - - + +
156C THR* 6.0 0.2 - - - -
159C ASP* 3.8 19.8 + - - +
162C GLN* 2.7 30.8 + - - -
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Residues in contact with LYS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLU 3.3 11.2 + - - +
107C ASP* 3.1 11.6 + - - +
109C LYS* 1.3 75.5 - - + +
111C THR* 1.3 63.0 + - - +
112C GLU* 3.9 1.2 + - - -
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Residues in contact with THR 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ASP* 2.8 22.9 + - - -
108C TYR* 3.2 14.4 + - - -
109C LYS 3.9 5.9 - - - +
110C LYS* 1.3 81.5 - - - +
112C GLU* 1.3 79.2 + - + +
113C SER 3.7 1.6 + - - -
115C LEU* 4.2 19.5 - - + +
116C LEU* 3.7 24.1 - - + +
119C LYS* 3.1 36.8 - - - -
155C PRO* 5.9 1.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il